Chem153A

Biochemistry: Introduction to Structure, Enzymes and Metabolism

Exam 1
Name: Date:

Instructions: Refer to page 10 for pKa values to use in Exam1. Limit your answers to 2
brief sentences. Graders are not required to grade more than 2 sentences per question.
This exam is open notes/ book. Follow the honor code specified in the syllabus.

1. Label the following statements as True or False (4 points):

a. Bacteria lack membrane bound organelles; however, they contain a well-
defined nucleus. ____________
b. Gram positive bacteria have a thick peptidoglycan layer. __________
c. The mitochondrion is the location of protein synthesis. __________
d. The Golgi apparatus is the site of protein processing and packaging.
__________

2. Below are 2 free energy diagrams for 2 different reactions. State whether each
diagram is exergonic or endergonic. Label the 5 arrows correctly based upon the
below choices, which may or may not be used more than once. (6 points)
a. ΔG
b. ΔG‡catalyzed
c. ΔG‡
d. ΔG‡uncatalyzed

Reactants
Products

ΔG ΔG

Reactants
Products

Reaction progress A→ B Reaction progress A→ B

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 3. Identify the functional groups that are circled (and in the triangle) in the diagram
below (4 points).

4. Can a reaction that is nonspontaneous with a ΔGo value of +20 kJ/mol be made
to become favorable? If so, then how? (4 points)
.

5. Draw the species of alanine that dominates at pH 1.0. Circle the stationary phase
that will better retain the species that dominates at pH 1.0, and state whether the
circled stationary phase is a cation exchanger or anion exchanger. (6 points)

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6. Calculate the ratio of conjugate base to weak acid at pH 7.0 for a molecule with a
pKa of 8.2. (6 points)

7. What is the name of the buffering system that buffers the blood and cytoplasm of
the cell, respectively? (5 points)
a. Bicarbonate only
b. Bicarbonate and phosphate
c. Phosphate and ammonium
d. None of the above

8. Is the following compound more water soluble in an aqueous solution of 0.1 M

NaOH or 0.1 M HCl? Briefly explain why. (5 points)

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9. Draw the structure of the oligopeptide V-M-R at pH 10. (5 points)

10. What is the net charge of the oligopeptide N-E-Y at pH 7.5? (5 points)

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11. Calculate the pI of the oligopeptide M-K-S. (5 points)

12. Below is the Ramachandran plot depicting the location of several secondary
structures. Draw the phi dihedral angle for parallel β sheets in the designated
box. Also state the degree of the dihedral angle in the box. Use the structure of a
dihedral angle below (adjacent to the Ramachandran plot) as a model to draw
your dihedral angle. (5 points)

Model Dihedral angle

Phi dihedral angle for antiparallel beta sheet

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13. A polyaspartate polypeptide, made of only L-Asp residues, adopts a random coil
structure at a pH above 7.0; however, it adopts an alpha helix conformation at pH
of 2.0. Provide a brief explanation of this phenomenon. (5 points)

14. The process of hair, which is made up of α-keratin helices, getting permed is
depicted in the diagram below in box 1. Circle the reagent in Box 2 that will most
likely be used in step1 of Box 1. (5 points)

Box 1

1 2 3

Box 2

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15. Briefly explain how the heme protoporphyrin ring changes from the
deoxygenated state to the oxygenated state of hemoglobin. (5 points)

16. Below is a list of hypothetical Hemoglobin variants. Circle the name of the variant
that is most likely to show an increase in BPG binding. Does such a hypothetical
variant cause an increase or decrease in hemoglobin’s affinity for oxygen? (5
points)
a. Hb Minnesota: substitutes Pro for Leu in an alpha helix
b. Hb Towncow: substitutes Lys for Val
c. Hb New Orleans: substitutes Met for Tyr, which disrupts the hydrogen
bonding at the α1β1 interface.
d. All of the above

17. Below is a rate vs [substrate] curve for the enzyme aspartate transcarbamolyase
(ATCase). ATP is known to stabilize the R-state of ATCase and makes it easier
for the aspartate substrate to bind. While CTP, on the other hand stabilizes the T-
state of ATCase. Draw the curves for the binding of ATP and CTP and label the
curves clearly with ATP or CTP. (4 points)

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 18. Enzyme X follows simple Michaelis-Menten kinetics and has different affinities for
substrates A and B. Km for substrate A is equal to 20mM and the Km for
substrate B is 15mM. What is the preferred substrate for enzyme X? (5 points)

19. Below is a Lineweaver-Burke plot for an enzyme in the absence and presence of
an inhibitor. Calculate Vmax apparent and Km Apparent for the graph. (6 points)

0.6

0.5

0.4

0.3

0.2

0.1

0.0
-0.05 -0.04 -0.03 -0.02 -0.01 0.00 0.01 0.02 0.03 0.04 0.05 0.06

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20. Based upon the graph in question 17, what type of inhibitor is depicted, and does
this inhibitor have a greater affinity for the enzyme only, enzyme-substrate
complex only, or both? (5 points)

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Functional Group pKa
Terminal α-carboxyl group 3.0
Terminal α-amino group 8.0
α-carboxyl (free amino acid) 2.0
α-amino (free amino acid) 9.5
Aspartic acid 4.1
Glutamic acid 4.1
Histidine 6.0
Cysteine 8.3
Tyrosine 10.0
Lysine 10.5
Arginine 12.5

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